Merge branch 'master' of github.com:scalableminds/webknossos into account-settings-page

Author: hotzenklotz

CHANGELOG.unreleased.md

@@ -19,6 +19,8 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 ### Fixed
 - Improved efficiency of saving bounding box related changes. [#8492](https://github.com/scalableminds/webknossos/pull/8492)
 - When deleting a dataset, its caches are cleared, so that if a new dataset by the same name is uploaded afterwards, only new data is loaded. [#8638](https://github.com/scalableminds/webknossos/pull/8638)
+- Fixed a race condition when starting proofreading with a split action. [#8676](https://github.com/scalableminds/webknossos/pull/8676)
+- Fixed that activating a mapping got stuck when a dataset was opened in "view" mode. [#8687](https://github.com/scalableminds/webknossos/pull/8687)
 
 ### Removed
 

MIGRATIONS.unreleased.md

@@ -8,5 +8,7 @@ User-facing changes are documented in the [changelog](CHANGELOG.released.md).
 ## Unreleased
 [Commits](https://github.com/scalableminds/webknossos/compare/25.06.1...HEAD)
 
+- The default thread pool size was increased from 5 to 10 times the number of available CPUs (capped at 1000). Note that wk may need slightly more memory because of this. [#8686](https://github.com/scalableminds/webknossos/pull/8686)
+
 ### Postgres Evolutions:
 - [134-dataset-layer-attachments.sql](conf/evolutions/134-dataset-layer-attachments.sql)

conf/application.conf

@@ -66,12 +66,12 @@ play {
 pekko.actor.default-dispatcher {
   # We use a compromise for our thread pool configuration
   # Parts of our api are async, so they should not need many threads,
-  # but some parts are also blocking (file io, gcs, s3 access), causing new requests
+  # but some parts are also blocking (some file io, gcs access), causing new requests
   # to wait despite idle cpu, if there are too few threads
   fork-join-executor {
-    parallelism-factor = 5.0 # Thread count = ceil(available processors * factor)
+    parallelism-factor = 10.0 # Thread count = ceil(available processors * factor)
     parallelism-min = 8 # Min number of threads to cap factor-based parallelism number to
-    parallelism-max = 300 # Max number of threads to cap factor-based parallelism number to
+    parallelism-max = 1000 # Max number of threads to cap factor-based parallelism number to
   }
 }
 

frontend/javascripts/admin/rest_api.ts

@@ -1,6 +1,6 @@
 import dayjs from "dayjs";
 import { V3 } from "libs/mjs";
-import type { RequestOptions } from "libs/request";
+import type { RequestOptions, RequestOptionsWithData } from "libs/request";
 import Request from "libs/request";
 import type { Message } from "libs/toast";
 import Toast from "libs/toast";
@@ -90,6 +90,7 @@ import type {
   MappingType,
   NumberLike,
   PartialDatasetConfiguration,
+  SaveQueueEntry,
   StoreAnnotation,
   TraceOrViewCommand,
   UserConfiguration,
@@ -2398,3 +2399,12 @@ export function requestVerificationMail() {
     method: "POST",
   });
 }
+
+export function sendSaveRequestWithToken(
+  urlWithoutToken: string,
+  data: RequestOptionsWithData<Array<SaveQueueEntry>>,
+): Promise<void> {
+  // Ideally, this function should be refactored further so that it generates the
+  // correct urlWithoutToken itself.
+  return doWithToken((token) => Request.sendJSONReceiveJSON(`${urlWithoutToken}${token}`, data));
+}

frontend/javascripts/libs/utils.ts

@@ -1303,3 +1303,11 @@ export function getPhraseFromCamelCaseString(stringInCamelCase: string): string
     .map((word) => capitalize(word.replace(/(^|\s)td/, "$13D")))
     .join(" ");
 }
+
+export function areSetsEqual<T>(setA: Set<T>, setB: Set<T>) {
+  if (setA.size !== setB.size) return false;
+  for (const val of setA) {
+    if (!setB.has(val)) return false;
+  }
+  return true;
+}

frontend/javascripts/test/api/api_skeleton_latest.spec.ts

@@ -8,10 +8,9 @@ import { vi, describe, it, expect, beforeEach } from "vitest";
 import type { Vector3 } from "viewer/constants";
 import { enforceSkeletonTracing } from "viewer/model/accessors/skeletontracing_accessor";
 
-// All the mocking is done in the helpers file, so it can be reused for both skeleton and volume API
 describe("API Skeleton", () => {
   beforeEach<WebknossosTestContext>(async (context) => {
-    await setupWebknossosForTesting(context, "skeleton");
+    await setupWebknossosForTesting(context, "skeleton", { dontDispatchWkReady: true });
   });
 
   it<WebknossosTestContext>("getActiveNodeId should get the active node id", ({ api }) => {

frontend/javascripts/test/api/api_volume_latest.spec.ts

@@ -7,7 +7,6 @@ import {
 } from "../fixtures/volumetracing_server_objects";
 import { AnnotationTool } from "viewer/model/accessors/tool_accessor";
 
-// All the mocking is done in the helpers file, so it can be reused for both skeleton and volume API
 describe("API Volume", () => {
   beforeEach<WebknossosTestContext>(async (context) => {
     await setupWebknossosForTesting(context, "volume");

frontend/javascripts/test/backend-snapshot-tests/annotations.e2e.ts

@@ -11,7 +11,7 @@ import { createTreeMapFromTreeArray } from "viewer/model/reducers/skeletontracin
 import { diffTrees } from "viewer/model/sagas/skeletontracing_saga";
 import { getNullableSkeletonTracing } from "viewer/model/accessors/skeletontracing_accessor";
 import { getServerVolumeTracings } from "viewer/model/accessors/volumetracing_accessor";
-import { sendRequestWithToken, addVersionNumbers } from "viewer/model/sagas/save_saga";
+import { addVersionNumbers } from "viewer/model/sagas/save_saga";
 import * as UpdateActions from "viewer/model/sagas/update_actions";
 import * as api from "admin/rest_api";
 import generateDummyTrees from "viewer/model/helpers/generate_dummy_trees";
@@ -174,7 +174,7 @@ describe("Annotation API (E2E)", () => {
   });
 
   async function sendUpdateActions(explorational: APIAnnotation, queue: SaveQueueEntry[]) {
-    return sendRequestWithToken(
+    return api.sendSaveRequestWithToken(
       `${explorational.tracingStore.url}/tracings/annotation/${explorational.id}/update?token=`,
       {
         method: "POST",

frontend/javascripts/test/fixtures/skeletontracing_server_objects.ts

@@ -5,11 +5,11 @@ import {
   type APITracingStoreAnnotation,
 } from "types/api_types";
 
-const TRACING_ID = "47e37793-d0be-4240-a371-87ce68561a13";
+const TRACING_ID = "skeletonTracingId-47e37793-d0be-4240-a371-87ce68561a13";
 
 export const tracing: ServerSkeletonTracing = {
   typ: AnnotationLayerEnum.Skeleton,
-  id: "47e37793-d0be-4240-a371-87ce68561a13",
+  id: TRACING_ID,
   trees: [
     {
       treeId: 2,

frontend/javascripts/test/fixtures/tasktracing_server_objects.ts

@@ -5,7 +5,7 @@ import {
   type APITracingStoreAnnotation,
 } from "types/api_types";
 
-const TRACING_ID = "e90133de-b2db-4912-8261-8b6f84f7edab";
+const TRACING_ID = "skeletonTracingId-e90133de-b2db-4912-8261-8b6f84f7edab";
 export const tracing: ServerSkeletonTracing = {
   typ: "Skeleton",
   trees: [
@@ -42,7 +42,7 @@ export const tracing: ServerSkeletonTracing = {
         b: 0,
         a: 1,
       },
-      name: "",
+      name: "", // there is a test that asserts that empty names will be renamed automatically
       isVisible: true,
       createdTimestamp: 1528811979356,
       metadata: [],
@@ -65,27 +65,27 @@ export const tracing: ServerSkeletonTracing = {
   },
   additionalAxes: [],
   zoomLevel: 2,
-  id: "e90133de-b2db-4912-8261-8b6f84f7edab",
+  id: TRACING_ID,
 };
 export const annotation: APIAnnotation = {
-  datasetId: "66f3c82966010034942e9740",
+  datasetId: "datasetId-66f3c82966010034942e9740",
   modified: 1529066010230,
   state: "Active",
-  id: "5b1fd1cf97000027049c67ee",
+  id: "annotationId-5b1fd1cf97000027049c67ee",
   name: "",
   description: "",
   stats: {},
   typ: "Task",
   task: {
-    id: "5b1fd1cb97000027049c67ec",
+    id: "taskId-5b1fd1cb97000027049c67ec",
     projectName: "sampleProject",
     projectId: "dummy-project-id",
     team: "Connectomics department",
     type: {
       id: "5b1e45faa000009d00abc2c6",
       summary: "sampleTaskType",
       description: "Description",
-      teamId: "5b1e45f9a00000a000abc2c3",
+      teamId: "teamId-5b1e45f9a00000a000abc2c3",
       teamName: "Connectomics department",
       settings: {
         allowedModes: ["orthogonal", "oblique", "flight"],
@@ -98,7 +98,7 @@ export const annotation: APIAnnotation = {
       recommendedConfiguration: null,
       tracingType: "skeleton",
     },
-    datasetId: "66f3c82966010034942e9740",
+    datasetId: "datasetId-66f3c82966010034942e9740",
     datasetName: "ROI2017_wkw",
     neededExperience: {
       domain: "oxalis",
@@ -156,7 +156,7 @@ export const annotation: APIAnnotation = {
   tracingTime: null,
   tags: ["ROI2017_wkw", "skeleton"],
   owner: {
-    id: "5b1e45faa00000a900abc2c5",
+    id: "userId-5b1e45faa00000a900abc2c5",
     email: "sample@scm.io",
     firstName: "Sample",
     lastName: "User",
@@ -165,7 +165,7 @@ export const annotation: APIAnnotation = {
     isDatasetManager: true,
     teams: [
       {
-        id: "5b1e45f9a00000a000abc2c3",
+        id: "teamId-5b1e45f9a00000a000abc2c3",
         name: "Connectomics department",
         isTeamManager: true,
       },
@@ -176,7 +176,7 @@ export const annotation: APIAnnotation = {
   isLockedByOwner: false,
   teams: [
     {
-      id: "5b1e45f9a00000a000abc2c3",
+      id: "teamId-5b1e45f9a00000a000abc2c3",
       name: "Connectomics department",
       organization: "Connectomics department",
     },